The amount doubles the $7.5 million in assistance that Foreign Minister Fumio Kishida pledged during a visit to Brussels in January.
Kishida said in a statement the aid was part of Japan's effort to support "counter-terrorism capacity building assistance in the Middle East/Africa," including border control, investigation and development of legal systems.
Vice foreign minister Yasuhide Nakayama will give details on the aid when he attends a global counter-terrorism conference later this week in Washington, ministry officials said.
The announcement comes weeks after a Japanese journalist and his adventurer friend were decapitated by extremists from the self-styled Islamic State, a group whose fighters control tracts of Syria and Iraq.
Prime Minister Shinzo Abe has come in for criticism over the timing of an earlier $200 million Japanese pledge to help refugees fleeing IS-controlled areas.
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Abe announced the cash in Egypt on January 17, saying Japan would "help curb the threat" of IS and give the money "for those countries contending with" the militants.
Days later a video emerged in which a masked man demanded the same sum as a ransom for the life of the two Japanese hostages.
Over the following tense weeks, Abe repeatedly said Japan would not "give in to terrorism".
The militants later changed their demand to the release of a death row inmate from a Jordanian prison.
Tokyo pressed Jordan for its help, but the militants eventually announced the killing of the pair as well as a Jordanian airman, along with photos and videos.
Japan hopes to demonstrate its continued resolve with the fresh assistance, the Sankei Shimbun newspaper said, adding that the money would be distributed through international organisations to affected regions, including countries bordering Syria and Iraq.